本文排版定稿已在中国知网网络首发,如需阅读全文请打开知网首页,并搜索该论文题目即可查看。
南川梅花草叶绿体基因组密码子偏好性分析
Analysis of Codon Usage Bias in Chloroplast Genome of Parnassia amoena
-
摘要: 为揭示南川梅花草叶绿体基因组密码子使用模式及主要影响因素,以南川梅花草叶绿体基因组全序列为研究对象,通过剔除重复基因等筛选步骤,最终得到44条基因编码序列(coding DNA sequence, CDS),利用Codon W 1.4.2软件和CUSP程序等对其进行密码子碱基组成分析、中性绘图分析、有效密码子数(ENC-plot)分析、奇偶偏好(PR2-plot)分析和最优密码子分析。结果表明:南川梅花草叶绿体基因组密码子3个位置上的GC含量呈现GC1>GC2>GC3的趋势,说明密码子末尾碱基偏好以A/T(U)结尾;基因组有效密码子数(ENC)均值为48.05,表明南川梅花草叶绿体基因组密码子使用偏好性较弱。ENC和GC3之间呈极显著正相关,说明密码子第3位碱基的组成对该物种密码子使用偏好性具有显著影响;偏好性受到48.15%的突变压力和51.85%的选择压力,结合ENC-plot和PR2-plot分析进一步说明,碱基突变与自然选择共同影响该种叶绿体基因组的密码子使用模式,但自然选择的影响更大。南川梅花草叶绿体基因组含UUA、AUU、GUA等19个最优密码子,大多以U结尾,其余以A结尾。Abstract: To investigate the codon usage pattern and major influencing factors in the chloroplast genome of Parnassia amoena, the complete chloroplast genome of P. amoena was used as the research object. Through screening and removing duplicate genes, a total of 44 coding DNA sequences (CDS) were ultimately obtained. These sequences were analyzed using Codon W 1.4.2 and CUSP programs, including assessments of codon base composition, neutral plot analysis, ENC-plot analysis, PR2-plot analysis, and optimal codon identification. The results showed that the GC content at the three positions of codons in the chloroplast genome of P. amoena was GC1>GC2>GC3, indicating a preference for A/T (U) at the end of codons. The average effective number of codons (ENC) in the genome was 48.05, indicating a relatively weak codon usage bias in P. amoena. In the correlation analysis, a highly significant positive correlation was observed between ENC and GC3, suggesting that the nucleotide composition at the third codon position influences codon usage bias. The neutral plot results showed the codon usage bias is influenced by 48.15% mutation pressure and 51.85% selection pressure. Combined with ENC-plot and PR2-plot analyses, it further indicates that both base mutation and natural selection jointly influence the codon usage pattern in the chloroplast genome of this species, with natural selection playing a dominant role. Furthermore, optimal codon analysis identified 19 optimal codons (including UUA, AUU, and GUA) in the P. amoena chloroplast genome, most of which terminate with U, while the remainder end with A. The results of this study will provide theoretical references for the research on molecular evolution mechanism and chloroplast genetic engineering of P. amoena, and to lay a foundation for the study of systematic evolution of Parnassia.